This game has a very strange scoring system. I still don't know what makes the large enemies worth more points when you kill them, though the point values are fixed values.
However, I do know this:
Shooting down airborne enemies and having them crash into ground enemies will give you insane point bonuses:
Normal tanks are worth 96,000 points
Medium tanks are worth 192,000 points
The tank midboss in Stage 1, if you kill it with an airborne enemy wreck, is worth a whopping 48 million points.
Grounded large planes in stage 2 are worth 12-15 million points.
Myself and Malc went through this back when it first showed up. We never could work out how sometimes round 1 scores were HUGELY higher than normal, although clearly we'd been doing /something/ differently. Maybe it's a bug.
We also never worked out how to reliably trigger the green train in Cyvern, which I now wish I had never sold, and will have to source a new one of. Drat.